The inflammatory bowel diseases (IBD), composed of Crohn's disease (CD) and ulcerative colitis (UC), result from an inappropriately directed inflammatory response to the enteric microbiota in a genetically susceptible host. Genome wide association studies (GWAS) have linked 163 specific single nucleotide polymorphisms (SNPs) to IBD disease pathogenesis. Within these associated loci, there are over 5000 additional SNPs that are in linkage disequilibrium (LD) with the identified SNPs, and it is not known which of these contribute to IBD. Most of these SNPs map to non-coding regions of the genome, suggesting that many variants contribute to IBD by modifying gene regulatory element activity. The role of environmental factors such as the enteric microbiota in the initiation and perpetuation of inflammation in IBD is incontrovertible. Specifically, loss of lamina propria (LP) macrophage tolerance to the enteric microbiota is a central event in the initiation and progression of chronic intestinal inflammation. We hypothesize that DNA variation that impacts gene regulatory element activity significantly contributes to the differential host response to microbial stimuli between normal and IBD individuals. The primary goal of this proposal is to identify genetic, regulatory activity, and gene expression changes that significantly contribute to IBD at molecular and clinical levels. Genomic regions of nucleosome-depleted, open chromatin have been linked to all types of regulatory elements, and genome-wide assays to detect these are now available. In Aim 1, we will determine open chromatin status, transcription levels, and genotypes for a panel of comprehensively phenotyped CD and UC patient tissue samples obtained from the non-inflamed section of the ascending colon. Similar data will be generated for non-IBD controls for comparison. Using these data, we will determine regulatory elements with genetically driven differential activity across a host of clinical and molecular IBD phenotypes. In Aim 2, we will uncover the molecular basis for loss of LP macrophage tolerance in CD by determining variation in active gene regulatory elements and gene expression levels between lamina propria (LP) macrophages in a subset of CD and UC patients and non-IBD controls in Aim 1. To understand how these differences translate to altered inflammatory response to bacteria, we will determine changes in chromatin status and expression in LP macrophages from CD, UC, and non-IBD patients when these cells are stimulated with an adherent-invasive E. coli (AIEC) strain previously isolated from CD patients and separately with E. faecalis. The long-term goals of this project are: 1) To fill the gap between our ability to detct genetic, chromatin, and gene expression variation linked to IBD and our ability to explain how that variation ultimately contributes to IBD; and 2) To provide a unique data resource for IBD investigators to access for their own studies.